{
  "_id": "6a1d27cd1d7bb097a0a3832b",
  "Package": "Rbec",
  "Type": "Package",
  "Title": "Rbec: a tool for analysis of amplicon sequencing data from\nsynthetic microbial communities",
  "Version": "1.21.0",
  "Authors@R": "person(\"Pengfan\", \"Zhang\", email = \"pzhang@mpipz.mpg.de\", role = c(\"aut\", \"cre\"))",
  "Description": "Rbec is a adapted version of DADA2 for analyzing amplicon\nsequencing data from synthetic communities (SynComs), where the\nreference sequences for each strain exists. Rbec can not only\naccurately profile the microbial compositions in SynComs, but\nalso predict the contaminants in SynCom samples.",
  "License": "LGPL-3",
  "RoxygenNote": "7.1.1",
  "biocViews": "Sequencing, MicrobialStrain, Microbiome",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev libjpeg-dev liblzma-dev\nlibpng-dev libx11-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:55:51 UTC",
  "RemoteUrl": "https://github.com/bioc/Rbec",
  "RemoteRef": "HEAD",
  "RemoteSha": "9c8c685c42ddc37bd909206ab72ff15cd9c61f06",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-30 09:33:30 UTC",
    "User": "root"
  },
  "Author": "Pengfan Zhang [aut, cre]",
  "Maintainer": "Pengfan Zhang <pzhang@mpipz.mpg.de>",
  "MD5sum": "1676b18844dfa29a3047afa724d12934",
  "_user": "bioc",
  "_type": "src",
  "_file": "Rbec_1.21.0.tar.gz",
  "_fileid": "16c497578b773479d22f5e81483864ece121e1601753777250bc5165c967ef98",
  "_filesize": 1611390,
  "_sha256": "16c497578b773479d22f5e81483864ece121e1601753777250bc5165c967ef98",
  "_created": "2026-05-30T09:33:30.000Z",
  "_published": "2026-06-01T06:33:49.696Z",
  "_jobs": [
    {
      "job": 78798376328,
      "time": 195,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307292800"
    },
    {
      "job": 78798376060,
      "time": 158,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78798376589,
      "time": 428,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7307317832"
    },
    {
      "job": 78798376049,
      "time": 160,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78798376461,
      "time": 397,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307312265"
    },
    {
      "job": 78798376034,
      "time": 91,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78798376567,
      "time": 485,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307260843"
    },
    {
      "job": 78798376018,
      "time": 88,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78798376246,
      "time": 415,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307253199"
    },
    {
      "job": 78798376280,
      "time": 310,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307211019"
    },
    {
      "job": 78798375974,
      "time": 153,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78798376308,
      "time": 293,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7307305157"
    },
    {
      "job": 78798376615,
      "time": 287,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307302079"
    },
    {
      "job": 78798376537,
      "time": 287,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307302034"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675688169",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Rbec",
  "_commit": {
    "id": "9c8c685c42ddc37bd909206ab72ff15cd9c61f06",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380951
  },
  "_maintainer": {
    "name": "Pengfan Zhang",
    "email": "pzhang@mpipz.mpg.de"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.6",
      "role": "Imports"
    },
    {
      "package": "dada2",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.21.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.20.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing",
    "microbialstrain",
    "microbiome",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 283,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Rbec"
  },
  "_searchresults": 6,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/Rbec.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "Contam_detect",
    "Rbec"
  ],
  "_help": [
    {
      "page": "Contam_detect",
      "title": "Reference-based error correction of amplicon sequencing data",
      "topics": [
        "Contam_detect"
      ]
    },
    {
      "page": "Rbec",
      "title": "Reference-based error correction of amplicon sequencing data",
      "topics": [
        "Rbec"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Rbec/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "dada2",
    "DelayedArray",
    "deldir",
    "doParallel",
    "farver",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "hms",
    "hwriter",
    "interp",
    "IRanges",
    "isoband",
    "iterators",
    "jpeg",
    "labeling",
    "lambda.r",
    "lattice",
    "latticeExtra",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "pwalign",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppParallel",
    "readr",
    "reshape2",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "ShortRead",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "tibble",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Rbec.Rmd",
      "filename": "Rbec.html",
      "title": "Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities",
      "author": "Pengfan Zhang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "How to use Rbec?"
      ],
      "created": "2021-03-08 15:42:15",
      "modified": "2021-04-22 09:53:18",
      "commits": 9
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "rbec",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-05-30T09:48:39.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "9c8c685c42ddc37bd909206ab72ff15cd9c61f06",
      "fileid": "c3fbe4b5ea0f12deae18c3636271304875fdaa234a7a57457d0d21b990c0e497",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675688169"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-05-30T09:47:52.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "9c8c685c42ddc37bd909206ab72ff15cd9c61f06",
      "fileid": "d2af0efddacc027e5b8a54b58d1c3fbbdbbac172025b200cc3f9c6a8d1a81582",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675688169"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-05-30T09:37:59.000Z",
      "arch": "x86_64",
      "commit": "9c8c685c42ddc37bd909206ab72ff15cd9c61f06",
      "fileid": "af0cd91907db4d562f45d863935a969fdd60dad871dc4e6551a927f81feb0745",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675688169"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-05-30T09:37:09.000Z",
      "arch": "x86_64",
      "commit": "9c8c685c42ddc37bd909206ab72ff15cd9c61f06",
      "fileid": "fa8f27d2b12f45fffa60686bbf8ace5722ea6bfd90d8cc858a095e5d18541651",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675688169"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-30T09:46:37.000Z",
      "arch": "x86_64",
      "commit": "9c8c685c42ddc37bd909206ab72ff15cd9c61f06",
      "fileid": "a5cd63fc35287272bbc6d16647ae6ddcb4159c7920ed05a22d6a2a4ebd925fb6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675688169"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-30T09:45:50.000Z",
      "arch": "x86_64",
      "commit": "9c8c685c42ddc37bd909206ab72ff15cd9c61f06",
      "fileid": "75d4584b9f5116312d1cb7a4d5805d24c329f4b2270a8b85f0099270077357aa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675688169"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-30T09:45:57.000Z",
      "arch": "x86_64",
      "commit": "9c8c685c42ddc37bd909206ab72ff15cd9c61f06",
      "fileid": "8a9dff819a3e4e1ed0f300057dc200170215192676836dbe0b259471934cfacc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675688169"
    }
  ]
}